When vital parts and precious pieces are missing, the gut has a difficult time doing what it’s supposed to do — protect you from infections and pathogens,keeping serotonin and melatonin in circulation, recycling cholesterol, and energizing the brain and muscles. In ancient times, the average human likely had an enormous load of microbes from daily exposures compared to modern lifestyles. Think about it? No cold storage — everything fermented and room temperature. No toilet paper. No C-sections (yes sadly both more moms and babies died). No pesticides or antibiotics which indiscriminately wipe out too many protective microbes. The modern gut is reeling from the deficit of these allies which touch and provide feedback to nearly every immunological, neurological and hormone pathway.

So let’s say you a had a couple courses of the pink syrup growing up (Amoxicillin) then 1-2 courses of Cipro for sinus or upper respiratory infections as an adult. Not much but what does the resultant gut microbiota look like? The infertile mom? The constipated babysitter? The morbidly obese CEO? The lymphoma patient? The athletic Ironman with alcohol-dependent ADHD? The pale boy who shot up the high school?

Amoxicillin will knock out beneficial Lactobacillus, Bifidobacteria, Enterococcus and Enterobacteria which may lead to overgrowths of opportunists and yeasts if the the microbiome fails to remain resilient, robust and able to recover.

The Cipro may then annihilate to extinction anything else that Amox failed to exterminate: the ginormous Clostridiales group and the major player Faecalibacteria (aka F. prausnitzii).

Decimating or disorienting F. prausnitzii isn’t a great idea. It works in parallel with Bacteroides to build up the thick epithelial-guarding mucus layer. It’s like stripping off your SKIN or scalping your gonads. Very very bad idea. F. prausnitzii is so big it is the largest, single species that composes a healthy gut: 3-6% of all fecal species.

For example in IBD (ulcerative colitis and Crohn’s), a huge chunk of Clostridiales is absent whether the diseases were in remission or acute stages. Past antibiotics may or may not have played a role per studies. Where did the Clostridiales go? Were they ever transferred at birth or did mom lack them all secondary to antibiotics, lack of healthy soil exposures, stress, sugar or a high refined carb SAD?

Bacteroides and Clostridiales are typically 1:1 in balance roughly speaking. By thrashing the Clostridiales leaves the more opportunistic and hearty Bacteroides to override symmetrical ecosystem stability. In ulcerative colitis and Crohn’s, what ends up occurring is Bacteroides breaching the mucus and directly attacking crypts, colonocytes and adhering like colonies of pathogenic vipers. They set up shop and don’t leave (look at ugy pictures). Re-establishment of an encompassing mucus layer is as important as getting Clostridiales back in the hood and re-creating parity.

Both Bacteroides and most of Clostridiales love to ultra-fast ferment resistant starches. Feeding a sick ecosystem is probably not as critical as first bringing order by returning absent allies back to prominence. Butyrate improves mucus linings but only if bifidobacteria and other commensals are properly located.

So you can see 3 views on the microbes in our gut. Unless you do functional medicine lab testing (GDX, Biohealth, Doctor’s Data), all miss the same things: yeasts, parasites, pathogens, and helminth worms. All 3 views show slightly different commensals and mutualists based on slightly different testing methodologies and diverse healthy control subjects that they tested. Actually, I like them all because you can see the variance and diversity and this reflects our ancestry and genetic evolution. What is clear is that research has finally shifted to testing non-healthy subjects and the evidence reveals vast absences in different diseases. Essentially in nearly any disease, researchers find missing mutualists and commensals — all the above.

Vast extinctions. Empty tropical rainforests. Barren tundras.

Now you are starting be aware of what is gone. What does one have to do to find and recover stolen gems and diamonds? One can’t redo birth and squeeze down lactobacilli-coated slides or start licking porcelain bowls which harbor worms or parasites.

Am I correct in saying that you believe high levels of Clostridia spp. is always a positive? I just received by 2200 results back {entire report below} and my Clostridia was 5.9, while my Lactobacillus is very low vs. the Bifido. My advisor felt these needed to be brought back in balance and suggested stopping any Bifido and adding Lacto species along with Mutaflor. {currently on Prescript Assist and RS}..However, from what you are posting and the Bulletproof interview with Richard and Tim, the belief is that Lacto could indeed be “Fat People” bacteria. Thanks! Mike 🙂

The plan sounds prudent. Do you have a lot going on? The elastase and malabsorption are significant to me as well. Do you think the pancreas inflamed?

Lacto can be opportunistic — it is higher in obese when there is dysbiosis (sibo)! Which Lacto were you considering? Have you read Mr. Heisenbug’s blog? L plantarum has many gut healing properties.

Have you heard of GCBC, good clostridia bad Clostridia? It’s my book that I haven’t published yet lol. You need some good Clostridia. If it was me I’d pound some AOR probiotic-3. E coli works co-op with Enterococcus which is AOR (formerly known as S. faecalis).

You won’t get anywhere without decent adrenals (and lower fungal loads). Focus on adrenals if you’re practitioner has not discussed yet. Sounds like an excellent course!

AOR, megaspore, L plantarum and many other probiotics are anti-fungal but they can only do so much with high fungal loads and resistant biofilms and low thyroid/adrenals. Body temps, gastric acidity, trypsin, etc are all vital parts of digestion that control yeasts and pathogens.

Do you plan on writing a detailed posts on that other big player in the gut microbiome, yeast? I’ve had remission 3 times now from CFS with supplements that could affect yeast. Biotin, Super Thisilyn, and S. Boulardii. Only to relapse. I’d love to know how to pursue that.

Thanks!David

aerobic1

Interesting post, Grace. Having committed premeditated murder by way of (13) IV Lyme treatments via IPT that incorporated a cocktail Rocephin (Ceftriaxone), Tygacil (Tigecycline) and Doxycycline (similar to tetracycline), it was of little surprise the damage (decrease) I did to my beneficial flora and the increase in commensal flora.

When I looked at the susceptibilities of each of these antibiotics there was no beneficial strain that was not susceptible to this concoction. After many months of repopulating the gut, my latest Doctors Data Comprehensive Stool Analysis/Parasitology x 2 has improved with the exception of bifidobacterium which shows no growth (NG). I find that interesting. I have been using 50 billion CFU of Klaire Labs Ther-Biotic Complete probiotic (http://www.klaire.com/prod/proddetail.asp?id=V775-12) daily along with fermented and cultured foods but still no bifidobacterium growth is evident. Perhaps it is time for a different approach?

I have no preconceived expectations that my microbiome will ever return to normal; whatever normal is. Through the eyes of Alessio Fasano, Jeroen Raes and others, return to a balanced flora is often difficult if not impossible to achieve.

Don’t give up so easily! It can take time and trying different probiotics. Maybe the Klaire labs ones just aren’t so great for bifido. You could try natren. Or any number of others. I would just consider that your improvements mean you’re headed in the right direction and that is great! It means change and improvement is possible. I wouldn’t get all negative and low expectations just because everything was not better this time.

Steve

Hi Grace,

I started AOR-3 in addition to PrimalD (which I’ve been on for several years). Also eating a fair amt of RS…all with the hopes of improving my crohn’s. since starting the aor-3, my stools are much smaller, which is positive for me, but I have been passing a large amount of mucus. prior to the aor3 I was having several large stools daily. i’ve only been on 1 cap/day of the aor-3 for a month now and not sure if I should continue, reduce the dose, increase the dose? otherwise, I’m feeling good. not sure what to think of all this mucus? does anyone have any thoughts? thanks in advance!

I had a serious psoriasis flare which threatened to take over my body about a year ago. I went to the doctor very reluctantly and specifically asked for an antibiotic to stop the spread. He prescribed minomycin which in a matter of days not only stopped the spread, but completely cleared my skin. I am now on the AIP pale diet which has helped tremendously with the psoriatic arthritis, but has not so far done too much for the actual psoriasis. What “bugs” would destroy the nasty bacteria that promotes psoriasis? Any speculation? I would appreciate any thoughts along these lines. Thanks for your time.

Hi Grace,Thank you for all the great work you do! Your insights are amazing and I know if I can keep up with you I may just be able to put my AI in remission.

I have hashi’s and a very bad gut…have been severely constipated since youth. (sent my gi effects a few months ago) I also believe my adrenals are toast so your recent reply on those being critical to gut rehab is of great interest. I’ve been using the protocol with prescript assist, aor and primal defense, potato flour and psyllium, with little improvement. Wondering if you could provide some guidance on where to find a proper adrenal protocol…I’m tapped out on the D.O’s and naturo’s..lots of tests not a lot of results unfortunately. Thanks,Marianne

Hi Grace, One correction: You say “Norm Robillard talks about how Cipro may have contributed to the start of his health odyssey and GERD” If you give a second listen, I talk about Cipro, but just as an example of a lifesaving drug. I worked on the development of this antibiotic but did not take it. Cipro had nothing to do with my developing GERD.

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